{"entity": "researcher", "timestamp": "2026-08-15T12:54:31.155Z", "family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "affiliations": ["SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c"}}, "publications": [{"entity": "publication", "iuid": "18ed7dda17774ed28651b0abac78c7f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18ed7dda17774ed28651b0abac78c7f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18ed7dda17774ed28651b0abac78c7f7"}}, "title": "Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.", "authors": [{"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Zeis", "given": "Patrice", "initials": "P", "orcid": "0000-0001-7615-2201", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9cd91e9e23f74093903c94117303a485.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Alekseenko", "given": "Alisa", "initials": "A"}, {"family": "F\u00fcrst", "given": "Eliska", "initials": "E", "orcid": "0000-0001-7101-5347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/322dcf90ca3249e5bcf75bc6fcf8c9df.json"}}, {"family": "Sanchez", "given": "Yerma Pareja", "initials": "YP"}, {"family": "Lin", "given": "Gen", "initials": "G", "orcid": "0000-0001-9969-8418", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28ac170431ce4b8cb65ea783ecdb5154.json"}}, {"family": "Tekkedil", "given": "Manu M", "initials": "MM"}, {"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-02-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "910", "issn-l": "2041-1723"}, "abstract": "Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.", "doi": "10.1038/s41467-023-36586-x", "pmid": "36801853", "labels": {"SciLifeLab Fellow": null, "Vicent Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9936472"}, {"db": "pii", "key": "10.1038/s41467-023-36586-x"}], "notes": [], "created": "2023-05-29T07:36:20.218Z", "modified": "2023-05-29T07:36:20.350Z"}, {"entity": "publication", "iuid": "127ab2b4417f4ac0ace77e0f2c278dbc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc"}}, "title": "TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Marques", "given": "Sueli", "initials": "S", "orcid": "0000-0003-3368-4392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36fa155444764068a6515a6ec93a7a2e.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "18", "pages": "e104"}, "abstract": "Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.", "doi": "10.1093/nar/gkaa691", "pmid": "32816037", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "5894951"}, {"db": "pmc", "key": "PMC7544212"}], "notes": [], "created": "2020-11-08T15:50:59.020Z", "modified": "2022-11-04T11:32:14.267Z"}]}